Contacts of the helix formed by residues 147 - 163 (chain B) in PDB entry 5EJC
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 147 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B MSE 4.8 2.1 - - - +
82B LYS* 5.2 3.9 - - - -
145B VAL* 3.5 2.4 - - + +
146B GLU* 1.3 81.1 - - + +
148B SER* 1.3 59.7 + - - +
149B VAL* 3.7 13.9 + - - +
150B ASP* 3.0 44.4 + - + +
151B CYS* 2.8 36.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B TYR* 3.6 23.5 - - - -
104B GLN* 4.3 6.9 + - - -
108B TYR* 3.2 24.4 + - - -
146B GLU 3.3 6.3 + - - -
147B ASP* 1.3 75.8 + - - +
149B VAL* 1.3 64.2 + - - +
151B CYS* 4.4 0.2 - - - -
152B TYR* 3.1 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B MSE 4.1 19.3 - - + -
81B ARG 4.2 12.8 - - - +
82B LYS* 4.4 23.1 - - + +
85B TYR* 3.9 32.3 - - + -
147B ASP* 3.3 14.6 + - - +
148B SER* 1.3 74.6 - - - +
150B ASP* 1.3 66.0 + - - +
152B TYR* 3.5 1.2 + - - +
153B TRP* 3.0 42.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ALA* 5.0 6.0 - - + +
61B LYS* 3.2 29.5 + - + +
78B MSE 3.1 26.6 - - - +
145B VAL* 3.6 19.7 - - + +
147B ASP* 3.0 25.9 + - + +
149B VAL* 1.3 72.7 - - - +
151B CYS* 1.3 60.2 + - - +
153B TRP* 3.7 4.1 - - - +
154B ILE* 2.8 45.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B TYR* 3.8 24.2 - - - +
138B ALA 4.5 1.1 - - - -
141B MSE 3.6 15.3 - - - +
142B GLU* 3.6 37.5 - - - -
145B VAL* 3.4 19.4 - - - +
147B ASP 2.8 21.7 + - - +
148B SER* 3.8 4.7 - - - +
150B ASP* 1.3 74.1 - - - +
152B TYR* 1.3 53.1 + - - +
154B ILE* 4.0 2.7 - - - +
155B THR* 2.5 39.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B TYR* 4.0 16.6 - + + -
108B TYR* 3.6 46.6 - + + -
111B MSE 3.5 41.1 - - + +
112B TYR* 3.5 4.0 + - + -
115B GLU* 3.0 40.1 + - - +
134B PHE* 4.9 2.9 - + - -
148B SER 3.1 15.4 + - - +
149B VAL 3.8 2.2 - - - +
150B ASP 3.3 0.2 - - - -
151B CYS* 1.3 79.1 - - - +
153B TRP* 1.3 76.2 + + - +
155B THR* 3.3 4.6 + - - -
156B ARG* 2.8 58.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LYS* 6.2 0.2 - - + -
66B ILE* 3.4 20.8 - - + +
78B MSE 5.9 0.9 - - + -
81B ARG* 3.2 69.7 + - + +
84B GLN* 3.4 40.2 - - + -
85B TYR* 4.7 3.6 - - + +
115B GLU* 4.8 2.9 - - - -
149B VAL* 3.0 37.5 + - + +
150B ASP* 4.0 3.6 - - - +
152B TYR* 1.3 96.2 - + - +
154B ILE* 1.3 61.4 + - - +
156B ARG* 3.5 33.5 - - - +
157B ARG* 3.1 45.9 + - + +
946D SER* 4.4 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ALA* 4.4 11.0 - - + +
60B TRP* 3.9 17.7 - - + -
61B LYS* 4.0 19.5 - - + -
64B LEU* 3.9 17.0 - - + +
66B ILE* 3.8 19.3 - - + -
141B MSE 3.6 27.1 - - + -
145B VAL* 3.8 24.0 - - + -
150B ASP* 2.8 30.9 + - + +
151B CYS 4.0 2.0 - - - +
153B TRP* 1.3 71.0 - - - +
155B THR* 1.3 58.7 + - - +
157B ARG* 3.3 0.5 + - - -
158B PHE* 2.8 36.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B TYR* 5.2 2.6 - - + -
134B PHE* 3.9 24.5 - - + +
137B ILE* 4.2 11.7 - - + -
138B ALA* 3.8 30.4 - - + +
141B MSE 3.4 22.6 - - - +
151B CYS* 2.5 26.7 + - - -
152B TYR* 3.6 6.4 - - - -
154B ILE* 1.3 76.2 - - - +
156B ARG* 1.3 64.0 + - - +
158B PHE* 3.6 3.7 - - - +
159B VAL* 2.9 31.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B GLN* 5.4 1.4 - - - +
112B TYR* 3.8 28.1 - - + +
115B GLU* 3.1 36.6 + - - +
116B SER* 5.5 2.8 - - - +
134B PHE* 4.8 8.0 - - - -
152B TYR* 2.8 50.8 + - + +
153B TRP* 3.5 37.4 - - + +
155B THR* 1.3 72.2 - - - +
157B ARG* 1.3 72.0 + - + +
159B VAL* 3.7 1.7 - - - +
160B ASN* 2.8 38.5 + - - +
946D SER* 5.1 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B LEU* 3.1 45.6 + - + +
65B GLY* 4.8 7.3 + - - -
66B ILE* 3.8 16.2 - - + -
153B TRP* 3.1 29.1 + - + +
154B ILE 4.2 1.3 - - - +
156B ARG* 1.3 99.2 - - + +
158B PHE* 1.3 59.5 + - - +
160B ASN* 3.0 32.3 + - - +
161B GLN* 3.0 30.3 + - - +
942D GLN* 5.5 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B TRP* 6.2 0.9 - + - -
64B LEU* 4.3 8.0 - - + +
137B ILE* 3.9 29.4 - - + -
141B MSE 5.4 4.3 - - - -
154B ILE* 2.8 27.1 + - + +
155B THR* 3.6 4.0 - - - +
157B ARG* 1.3 78.1 - - - +
159B VAL* 1.3 63.6 + - + +
161B GLN* 3.4 19.6 - - - +
162B LEU* 3.4 15.2 - - + +
210B CYS* 4.4 11.7 - - - -
224B TRP* 3.7 52.5 - + + -
227B VAL* 3.5 34.8 - - + -
228B VAL* 4.0 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B TYR* 4.1 11.4 - - + +
133B VAL* 6.0 3.4 - - + -
134B PHE* 4.0 34.5 - - + +
137B ILE* 4.1 36.3 - - + -
155B THR* 2.9 22.0 + - + +
156B ARG 3.8 1.8 - - - +
158B PHE* 1.3 73.5 - - + +
160B ASN* 1.3 66.4 + - - +
161B GLN 3.2 0.2 - - - -
162B LEU* 3.1 22.3 + - + +
163B ASN* 3.2 25.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B TYR* 5.2 9.3 + - + -
156B ARG* 2.8 27.2 + - - +
157B ARG* 3.0 29.8 + - - +
159B VAL* 1.3 76.4 - - - +
161B GLN* 1.3 56.4 + - - +
163B ASN* 3.3 8.7 + - - +
164B THR* 2.7 53.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B LEU 5.5 3.6 + - - -
64B LEU* 3.9 22.2 - - + +
157B ARG* 3.0 18.1 + - - +
158B PHE* 3.4 13.5 - - - +
159B VAL 3.2 0.2 - - - -
160B ASN* 1.3 78.1 - - - +
162B LEU* 1.3 58.1 + - + +
164B THR* 3.7 5.2 - - - -
165B LYS* 3.0 60.8 + - + +
166B TYR* 3.1 22.2 + - + -
227B VAL* 3.7 14.5 + - - +
228B VAL* 3.5 22.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B VAL* 5.6 1.1 - - + -
137B ILE* 4.3 15.0 - - + -
158B PHE* 3.4 20.2 - - + +
159B VAL* 3.1 15.0 + - + +
161B GLN* 1.3 77.1 - - + +
163B ASN* 1.3 64.8 + - - +
164B THR 3.4 0.4 - - - -
166B TYR* 3.3 50.4 - - + +
167B ARG* 3.5 1.9 + - - -
170B LEU* 3.8 23.9 - - + +
208B LYS 3.7 22.9 - - - +
210B CYS* 3.9 25.1 - - - -
227B VAL* 4.5 9.6 - - + -
232B CYS* 6.1 0.2 - - + -
235B LEU* 5.9 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B TYR* 3.9 11.7 + - - -
159B VAL* 3.2 31.3 + - - +
160B ASN* 3.3 8.5 + - - +
161B GLN 3.2 0.6 - - - -
162B LEU* 1.3 83.8 - - - +
164B THR* 1.3 66.5 + - + +
167B ARG* 3.9 25.3 + - - +
170B LEU* 5.8 0.3 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il